LOCUS       NZ_CP053762             1549 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain 506 plasmid pMHMC-011, complete sequence.
ACCESSION   NZ_CP053762
VERSION     NZ_CP053762.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07663113
            Assembly: GCF_013201485.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1549)
  AUTHORS   Hoffmann,M., Sanchez,M., Worley,J. and Bry,L.
  TITLE     clinical or host associated isolate for Shigella sonnei
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1549)
  AUTHORS   Hoffmann,M., Sanchez,M., Worley,J. and Bry,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAY-2020) CFSAN, US FDA, 5001 Campus Drive, College
            Park, MD 20740, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAR-2020
            Assembly Method                   :: HGAP v. 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 445.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013201485.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 06:48:10
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,497
            CDSs (total)                      :: 5,365
            Genes (coding)                    :: 4,629
            CDSs (with protein)               :: 4,629
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 736
            CDSs (without protein)            :: 736
            Pseudo Genes (ambiguous residues) :: 0 of 736
            Pseudo Genes (frameshifted)       :: 208 of 736
            Pseudo Genes (incomplete)         :: 523 of 736
            Pseudo Genes (internal stop)      :: 128 of 736
            Pseudo Genes (multiple problems)  :: 117 of 736
            Pseudo Genes (short protein)      :: 3 of 736
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053762.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..1549
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="506"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pMHMC-011"
                     /geo_loc_name="USA:Boston"
                     /collection_date="2017"
                     /collected_by="Brigham and Women's Hospital"
     gene            complement(371..847)
                     /locus_tag="COO90_RS27335"
                     /old_locus_tag="COO90_27145"
     CDS             complement(371..847)
                     /locus_tag="COO90_RS27335"
                     /old_locus_tag="COO90_27145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          927..1035
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.091"
                     /coverage="100.0"
                     /evalue="9.09e-49"
     Typing          complement(1231..1328)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.24e-44"
ORIGIN
        1 atggaaggcg cgaaaaacgc ttacagaggc tctcaggagg tcaagcgcgc cgatacccct
       61 aaccaggggc tttcaggtcg ccaggaaccg cgccagcccc ctgcaaagcc catttgcacg
      121 gaacaggcag ccatgcggtt ggtaggtggt cgtagaccgt cggtgttgca gcgatggggg
      181 tctggggttc tccccagacg gtttccggta gcgctcaagg cgctgccgga accgtggcgg
      241 ctcggttttt tctggagaac ggggagcaaa aacacgcaaa ggattttgag gcggcaaaag
      301 agcaatgcag gatagacaat catggtcaga acgttaacac gtagcccctg attgtccgcc
      361 tgccgctagc tcaatttgaa aacatggcca tgattcggcg ctgaatatca ccgtctttgt
      421 tgaccagtgt tttagtgaca aacgctgcat ggtttttcgt agtgttgtat cccttccaga
      481 cttcatgtgg atcgagggca tacgcacaaa ccttaccagc aacggggatt ctaactaatg
      541 cattttttga ttctaagtaa ttgagccacc gaataattgt gcttctgcta actccaagtt
      601 tttcagctag gaattgctga tccgcaacga cagcgccaca cgtaggatcg atatgctccg
      661 ctaaaaatga gtacagcttc agtgctgata tgccttggct atccttcagc agctctcgaa
      721 cacgttccca accttttggg gatacctgtg taaaccttga atttttcttt gcttcttcga
      781 gatcctcggt gtttttcttt gcctcatctg aaagttgttt cagtcgtttt tctgaatcaa
      841 taaacatgat tttttccctc tgaaaatccc atgcactaac gttggttcaa atctaagcca
      901 tcatgacaca tctgtgcaac accttgttgc gtgttgtcgc atccaggatg cgacaacgtt
      961 gtgtcatcct ggatgcgaca ggtaaataaa aaacacacta aaaaaacaac cacttacaaa
     1021 tcggcgtaaa agatctattc taggcaaggg tgttgcgtgc aacgcaacgc cctttggggg
     1081 tgtcggggcg aagccctgac ccagtcacgt agcgatagcg gagtgtatac tggcttactc
     1141 ctatgcaagc ctcgccagcc gtgatttttg ccagatttcg tggttttcac gttcaacagc
     1201 tccatcgtgt ttttgccgtc cgttcaccgt taaaacgcct cagaaatcgg gacaggatgt
     1261 gtaatcgtat aaccgcgcat gcacgccgat acgattacca cttggtcagg gcttcacccc
     1321 gacaccccac atcagtgcgt aagtgctcaa tgtggcttcc ggttctcttc cgcttcctcg
     1381 tcgattcgct cgctatgctc ggtcatcgac ttgcggcgag cgggatcacc tctcgcatgt
     1441 tgtcggtgat cccggtgttg ttcttttggg gatgagtcgc cagatagccc ctcaaacgcg
     1501 ctcaaaagct ctcagacgca cgaaacgggt tttagatgcc cgccagggc
//
